There is no real need to stop having overlap. When I started out I used to work on getting a perfectly planned, fully built up empire. Then you eventually start wars and pick up the AIs weirdly placed cities anyway.
So now I just focus on what is going to help me get ahead right now. If I have a suboptimal city placement that gets me gold in the fat cross right away, that means maybe I save 4 turns getting to sanitation, which means I get my next round of settlers out faster, which means I have more markets up faster, which means I beat the AI to Esus and Poisons, which means I have assassins out first, which means I get Aeron's Chosen, etc..